After receiving the AIO-3288, it was flashed with Android 5.0 and all the USB ports were working.
As soon as i flashed Ubuntu 14.04 on it, then the USB ports are not working.
On re-flashing android once again, the USB ports are still disabled.

I just had a similar problem - trying to use the update program to write to /dev/sda via the rockchip update program and specifying the CONTROL root=/dev/sda1.

No error messages during the upload or the data check - but I noticed the power light on the SSD I had plugged into the USB 3.0 port wasn't on. I tried the USB 2.0 ports too.

Basically, I had to scp the linuxrootfs-normal.img to the device when it was booted from eMMC. Then I used 'gnome_disks' to install that img to the usb device. Then resizefs2 to gain the whole partition size (after running something that resizefs suggested).

Then I took a parameter.txt file and commented out everything except the CONTROL line and specified root=/dev/sda1.

I flashed the param file via the update program, I believe the command I used was 'di -p parameter.txt' and rebooted.

I'm using a mixed environment of Macs, so the 'scp' was no issue - but I seem to recall the default /etc/sshd_config in 16.04 doesn't allow Authentication by password, so if you try to copy via another Ubuntu machine you will need to modify the directives and restart sshd on the FireFly.